In the aftermath of the War of 3039, the intelligence failures experienced by the Federated Suns and Lyran Commonwealth highlighted the need for coordination between the intelligence communities of both states. The leaders of the Federated Commonwealth Alliance initially intended to consolidate their intelligence agencies into a single, combined organization. Facing serious resistance from the establishment of both intelligence communities, the leadership decided instead to form an umbrella agency, allowing them the organization to coordinate while still operating independently. Thus, the FCIC was formed, under the overall command of the Intelligence Secretariat, and answerable only to the rulers of the Federated Commonwealth.[3][4][5][6] In addition to these three more established agencies, the Secretariat also supervised the Military Intelligence Division, the intelligence-gathering branch of what had been the LCAF.[7] During its existence, the Intelligence Secretariat effectively replaced the MIIO Liaison - termed MI7 - within that organization, informing the LIC of MIIO and DMI operations as needed.[8]

Among its many responsibilities, the Secretariat provided the AFFC's Marshal of the Armies with all pertinent intelligence reports, freeing the organizations under its command from the duty.[9] The Secretariat also apparently had Regional Coordinators, one for each of the AFFC Marches.[10]

The FCIC and the Intelligence Secretariat were effectively cut in half with the Lyran secession in 3057, and the agency was finally dissolved at the conclusion of the FedCom Civil War.[11] MI7 of the DMI once again became the liaison department with the DMI, although it had been expanded with former FCIC personnel.[12]

After Allard's assassination in January 3052, Alexi Mallory, another war hero who had been Allard's Deputy Secretary, was promoted to take his place. Apparently, Mallory, and by implication Allard, continued to serve as the head of MIIO even while serving as the Intelligence Secretary.[17][18][19]

Mallory retired in 3056, and was succeeded by Jerrard Cranston, who in reality was Galen Cox, Victor Steiner-Davion's aide and confidante.[20] Although he served as Steiner-Davion's top intelligence advisor, Cranston/Cox's status of Intelligence Secretary was apparently not known to the public at-large and other intelligence services, who knew him only as a top aide to Victor. It is implied that even the LIC was not fully aware of Cranston's position.[21][22][23]

Most notably, the Intelligence Secretariat apparently included the security personnel assigned to protect the ruling family. It was Intelligence Secretariat agents who handled the protection of Archon Melissa Steiner-Davion when she was assassinated in 3055.[24] This practice continued during the reign of Victor Steiner-Davion.[25] The Secretariat also had the responsibility to monitor the loyalty of military personnel, and had the authority to order transfers to avoid potential problems.[26]

The FCIC (and, by extension, the FCIS) apparently included a number of their own departments altogether separate from the three organizations they oversaw. These included the Office of Science and Technology, whose accomplishments included the development of the Infiltrator Mk. IIBattle Armor, which was primarily used for intelligence-gathering missions and reconnaissance work. This was accomplished in cooperation with the New Avalon Institute of Science, using the Star League-era Nighthawk Mk. XXI as the basis. But into production in March 3060, most of the first runs were distributed to the intelligence services. Even by the Word of BlakeJihad, approximately 40 percent of the Infiltrator Mk. IIs remained in service with the DMI and MIIO.[27][28][29]

The Intelligence Secretariat had its own Forensics Division, which was considered highly capable and reliable.[30]

The Secretariat also had a Psych Division, conducting assessments of the Federated Commonwealth's friends and enemies alike, such as in the case of Phelan Kell and Ciro Ramirez in January 3052.[31]

Public relations also appeared to be part of their responsibilities, specifically the concern that Victor Steiner-Davion was seen by the Lyran people as more "Davion" than "Steiner".[32]

The FCIS also investigated criminal dealings within planetary governments, such as in the extreme case of Boss Tybus of Dustball in 3048. The Secretariat intended to find the evidence to prove Tybus' criminal dealings, and then send a detachment of AFFC troops to remove him from power. This was apparently unsuccessful, however, as Tybus was not removed until the Clan Invasion.[33]

The FCIS even went so far as to employ mercenary special forces and freelance intelligence agents for select tasks, such as investigating the rogue Citizens for Davion Purity organization, a separatist movement on Mararn.[34]

Not long after the Fourth Succession War, the Federated Commonwealth Intelligence Command Network was envisioned to expedite communications across the vast super-state, using the famed Black Box communications devices. The network was maintained by the DMI's MI3 and the Narns of the LIC. The network was scheduled to go on-line shortly before the Lyran secession.[35][36] The fate of this network is unclear, but it may be assumed to have been dissolved thereafter.

In March 3056, the Intelligence Secretariat foiled an attempt to sabotage the newly constructed Federated-Boeing InterstellarWarShip facility at Galax. The attempted explosion might have set back the Commonwealth's WarShip production program by several years. The alleged perpetrator, a contractor with suspected Free Skye leanings, was quietly imprisoned.[37]

One of the FCIS most noted accomplishments remained unknown to the Inner Sphere at large until more than a decade after it occurred. The Forensics Division discovered by chance in late 3057 that Captain-GeneralThomas Marik had been replaced with an imposter in 3037.[30] This gave Victor Steiner-Davion a political advantage in his further dealings with Marik. Because of the impressive security of the Division, no one else would learn of this discovery outside of Victor's inner circle. The rest of the Inner Sphere would not learn of the duplicity until the Jihad.

Arguably the most important investigation undertaken by the Intelligence Secretariat during its existence was the investigation into the murder of Archon Melissa Steiner-Davion. The FCIS undertook this task itself, and with the cooperation of all three agencies, and the assistance of Fuh Teng of Cenotaph Stables on Solaris, Agent Curaltis successfully hunted down and captured the killer, though he was initially unable to present evidence of who hired this assassin.[38][39][40][41][42] Later, it was FCIS agents who assisted the assassin in his operation to eliminate Ryan Steiner, although the assassin would escape afterwards.[43] It would not be until near the end of the FedCom Civil War that Curaltis would obtain enough evidence to convincingly implicate Katherine Steiner-Davion in the death of her mother.

The challenges of the post-Clan Invasion Era pushed the FCIS to its absolute limit, and ultimately proved to be overwhelming. The single largest challenge faced by the Secretariat was the continued presence of interagency rivalries between the three relevant organizations, often with nationalist sentiments. In some cases, it was even alleged that field agents from different agencies had opened fired on each other while conducting operations. As such, the FCIS spent much of its time as a clearinghouse of information, adding another level of separation between the intelligence and the leadership.[44][45]

The leadership of the Commonwealth in the form of Archon-Prince Victor Steiner-Davion was focused on the Clan threat, and the challenge of sending operatives into the Clan Occupation Zones and obtaining the intelligence needed to reclaim those planets and off-set any new offensives was difficult in the extreme. At the same time, the internal threats to the united Federated Commonwealth were unprecedented during this period, as the Free Skye Movement and the Capellan-backed Zhanzheng de Guang were both well-organized and funded, and enjoyed popular support in the Federation of Skye and Sarna March, respectively. Other separatist movements also gained traction.

In many of the sources, the terms Intelligence Secretariat (or FCIS) and Federated Commonwealth Intelligence Command (or FCIC) appear to be used interchangeably.[27][28][29] In addition, the Secretariat is referred to as MI7 in some works.[2]

In an apparent oversight, page 91 of the 20 Year Update states that Justin Allard was the Secretary of the Federated Commonwealth Ministry of Intelligence (the FCMI).[47] This is contradicted by multiple sources, and the "FCMI" is not mentioned in any other work.

The Office of Science and Technology is mentioned only with respect to the Infiltrator Mk. II battle armor, and is not named in any other book.

There's virtually no mention of the Intelligence Secretariat or the FCIC after 3060, implying that the organization was already becoming redundant by that time.